[Chimera-users] tunnel surface

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 10 10:54:45 PDT 2017


Hi Richard,
You can change transparency of anything, see the “transparency” command and for an example, the “similar binding sites” image tutorial…
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html>

However, general advice re tunnel surfaces (I changed the e-mail subject line to be more useful):

It can be difficult to show the tunnel surface only.  Often people will use some separate plugin or program to calculate a tunnel surface rather than trying to specify which atoms’ molecular surface to show, since (as you may have observed) it is hard to figure out which atoms line that tunnel.

Some alternatives you can try with Chimera:

(1) CASTp  has pre-calculated pocket and tunnels for structures in the PDB, and if you are using some already-deposited structure from there, you can fetch the structure and results from CASTp by  using menu: File… Fetch by ID (specifying PDB ID in the CASTp option), or a command something like:

open castp:2gbp

… if your structure were PDB entry 2GBP.  That would bring up a dialog listing the various pockets and tunnels, and you can click on each to show its surface.  Or, if you are using a structure that is not in the PDB database (or it is, but for some reason CASTp doesn’t have results for it already) you can upload it to the CASTp webserver and get results back by email and then show them in Chimera as described in this page.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/castp.html>

However, this still uses the molecular surface atomic patches, so sometimes you will get raggedy edges.  The other ways I mention avoid that problem.

(2) 3V calculation.  The 3V webserver calculates a “density map” that fills pockets and tunnels, and then you can open this  map and show its isosurface in Chimera. It’s been a while since I tried this, but the “channel finder” sounds the most promising unless you already know the X,Y,Z coordinates of the tunnel of interest.

(3) A long time ago I also tried something called MolAxis, with some minor reformatting of its output required to show in Chimera.  Example results and description here in our Image Gallery, along with CASTp results for the same structure:
<http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>

Finally, if you use Pymol, I know people often use a plugin called “HOLE” with Pymol for this purpose.

I hope this helps,
 Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 9, 2017, at 12:56 PM, Richard Collins <rcollins at sickkids.ca> wrote:
> 
> Hi Elaine
> 
> Yes this helps, thanks.  I used control-click to select residues.
> 
> Is there a way to adjust the transparency of ribbons, helices and amino acids?
> 
> What I am trying to do is find all the residues along the tunnel of my molecule. It is a solid protein with a tunnel through the middle.  Using the SURFACE function shows only the outer surface.
> 
> I am wondering if there is a way to show only the tunnel surface and not the outer surface?  For now  I am using the PER-MODEL CLIPPING to slice through the middle.




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